In a nutshell, Sencha Cmd operates on source files, so it will need to be run against the source code instead of a served instance.

For script tags, the src attributes need to use relative addressing (relative to the markup file) for Sencha Cmd to resolve the address and combine them in to a build. This should be workable in production as well, but obviously takes some adjustments perhaps.

There are some lower-level ways to deal with just JS files, but to use the high-level "page" command of the compiler, the above is required. To go the lower-level route, you would still need file system access to the JS source tree(s) and would need to identify the script(s) that serve as the "top" of the dependency calculation (the page serves that role when using the "page" command).